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Open Access Highly Accessed Research article

Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES)

Corina J Shtir1, Paul Marjoram2, Stanley Azen2, David V Conti23, Loic Le Marchand4, Christopher A Haiman2 and Rohit Varma256*

Author Affiliations

1 Department of Human Genetics and Neuroscience, University of California - Los Angeles, Los Angeles, CA 90095-708822, USA

2 Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA

3 Department of Environmental Health, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA

4 Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, USA

5 Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA

6 Doheny Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA

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BMC Genetics 2009, 10:71  doi:10.1186/1471-2156-10-71

Published: 10 November 2009

Abstract

Background

Population structure and admixture have strong confounding effects on genetic association studies. Discordant frequencies for age-related macular degeneration (AMD) risk alleles and for AMD incidence and prevalence rates are reported across different ethnic groups. We examined the genomic ancestry characterizing 538 Latinos drawn from the Los Angeles Latino Eye Study [LALES] as part of an ongoing AMD-association study. To help assess the degree of Native American ancestry inherited by Latino populations we sampled 25 Mayans and 5 Mexican Indians collected through Coriell's Institute. Levels of European, Asian, and African descent in Latinos were inferred through the USC Multiethnic Panel (USC MEP), formed from a sample from the Multiethnic Cohort (MEC) study, the Yoruba African samples from HapMap II, the Singapore Chinese Health Study, and a prospective cohort from Shanghai, China. A total of 233 ancestry informative markers were genotyped for 538 LALES Latinos, 30 Native Americans, and 355 USC MEP individuals (African Americans, Japanese, Chinese, European Americans, Latinos, and Native Hawaiians). Sensitivity of ancestry estimates to relative sample size was considered.

Results

We detected strong evidence for recent population admixture in LALES Latinos. Gradients of increasing Native American background and of correspondingly decreasing European ancestry were observed as a function of birth origin from North to South. The strongest excess of homozygosity, a reflection of recent population admixture, was observed in non-US born Latinos that recently populated the US. A set of 42 SNPs especially informative for distinguishing between Native Americans and Europeans were identified.

Conclusion

These findings reflect the historic migration patterns of Native Americans and suggest that while the 'Latino' label is used to categorize the entire population, there exists a strong degree of heterogeneity within that population, and that it will be important to assess this heterogeneity within future association studies on Latino populations. Our study raises awareness of the diversity within "Latinos" and the necessity to assess appropriate risk and treatment management.